APP-RB: An efficient method for biological network querying based on rebuild procedure

Biological molecules (e.g. DNAs, RNs, proteins, etc.) do not function in isolation themselves but in a sophisticated manner of various interactions between them to carry out every biological processes in living cells. Data about these interactions are exponentially increased thanks to advanced technologies. Analyzing biological interaction networks is essential to get insights into how biological system works. Among analytics tasks querying a small network of interest against a well studied large-scale one is regarded as one of the most essential task and is proven to be a NP-complete problem. This paper presents an efficient biological network querying method called APP-RB, which is an improvement of the state-of-the-art biological network queyring method APPAGATO introduced in 2016 by taking advantages of FASTAn, an PPI alignment algorithm. Experimental results showed that our algorithm performed much better than the original APPAGATO. With these results, we hope that our proposed method APP-RB will be helpful to biologists and those who are interested in network comparison problems.